Index: src/utils/faSplit/faSplit.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/faSplit/faSplit.c,v
retrieving revision 1.35
retrieving revision 1.36
diff -b -B -U 1000000 -r1.35 -r1.36
--- src/utils/faSplit/faSplit.c	31 Mar 2007 19:38:16 -0000	1.35
+++ src/utils/faSplit/faSplit.c	22 May 2010 18:50:33 -0000	1.36
@@ -1,755 +1,755 @@
 /* faSplit - Split an fa file into several files.. */
 #include "common.h"
 #include "portable.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "dnautil.h"
 #include "obscure.h"
 #include "fa.h"
 #include "options.h"
 #include "bits.h"
 
 static char const rcsid[] = "$Id$";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faSplit - Split an fa file into several files.\n"
   "usage:\n"
   "   faSplit how input.fa count outRoot\n"
   "where how is either 'about' 'byname' 'base' 'gap' 'sequence' or 'size'.  \n"
   "Files split by sequence will be broken at the nearest fa record boundary. \n"
   "Files split by base will be broken at any base.  \n"
   "Files broken by size will be broken every count bases.\n"
   "\n"
   "Examples:\n"
   "   faSplit sequence estAll.fa 100 est\n"
   "This will break up estAll.fa into 100 files\n"
   "(numbered est001.fa est002.fa, ... est100.fa\n"
   "Files will only be broken at fa record boundaries\n"
   "\n"
   "   faSplit base chr1.fa 10 1_\n"
   "This will break up chr1.fa into 10 files\n"
   "\n"
   "   faSplit size input.fa 2000 outRoot\n"
   "This breaks up input.fa into 2000 base chunks\n"
   "\n"
   "   faSplit about est.fa 20000 outRoot\n"
   "This will break up est.fa into files of about 20000 bytes each by record.\n"
   "\n"
   "   faSplit byname scaffolds.fa outRoot/ \n"
   "This breaks up scaffolds.fa using sequence names as file names.\n"
   "       Use the terminating / on the outRoot to get it to work correctly.\n"
   "\n"
   "   faSplit gap chrN.fa 20000 outRoot\n"
   "This breaks up chrN.fa into files of at most 20000 bases each, \n"
   "at gap boundaries if possible.  If the sequence ends in N's, the last\n"
   "piece, if larger than 20000, will be all one piece.\n"
   "\n"
   "Options:\n"
   "    -verbose=2 - Write names of each file created (=3 more details)\n"
   "    -maxN=N - Suppress pieces with more than maxN n's.  Only used with size.\n"
   "              default is size-1 (only suppresses pieces that are all N).\n"
   "    -oneFile - Put output in one file. Only used with size\n"
-  "    -extra   - Add extra bytes at the end to form overlapping pieces.  Only used with size.\n"
+  "    -extra=N - Add N extra bytes at the end to form overlapping pieces.  Only used with size.\n"
   "    -out=outFile Get masking from outfile.  Only used with size.\n"
   "    -lift=file.lft Put info on how to reconstruct sequence from\n"
   "                   pieces in file.lft.  Only used with size and gap.\n"
   "    -minGapSize=X Consider a block of Ns to be a gap if block size >= X.\n"
   "                  Default value 1000.  Only used with gap.\n"
   "    -noGapDrops - include all N's when splitting by gap.\n"
   "    -outDirDepth=N Create N levels of output directory under current dir.\n"
   "                   This helps prevent NFS problems with a large number of\n"
   "                   file in a directory.  Using -outDirDepth=3 would\n"
   "                   produce ./1/2/3/outRoot123.fa.\n"
   "    -prefixLength=N - used with byname option. create a separate output\n"
   "                   file for each group of sequences names with same prefix\n"
   "                   of length N.\n"
 );
 
 }
 
 /* command line option specifications */
 static struct optionSpec optionSpecs[] = {
     {"maxN", OPTION_INT},
     {"oneFile", OPTION_BOOLEAN},
     {"out", OPTION_STRING},
     {"lift", OPTION_STRING},
     {"minGapSize", OPTION_INT},
     {"noGapDrops", OPTION_BOOLEAN},
     {"outDirDepth", OPTION_INT},
     {"prefixLength", OPTION_INT},
     {"extra", OPTION_INT},
     {NULL, 0}
 };
 
 static int outDirDepth = 0;
 
 off_t estimateFaSize(char *fileName)
 /* Estimate number of bases from file size. */
 {
 off_t size = fileSize(fileName);
 return 0.5 + size * 0.99;
 }
 
 off_t calcNextEnd(int fileIx, int totalFiles, off_t estSize)
 /* Return next end to break at. */
 {
 if (fileIx == totalFiles)
      return 0xefffffff;	/* bignum */
 else
     {
     off_t nextEnd = round((double)fileIx*(double)estSize/(double)totalFiles/16.0);
     return nextEnd<<4;
     }
 }
 
 void mkOutPath(char *outPath, char* outRoot, int digits, int fileCount)
 /* generate output file name */
 {
 char dir[PATH_LEN], fname[PATH_LEN];
 splitPath(outRoot, dir, fname, NULL);
 
 strcpy(outPath, dir);
 if (outDirDepth > 0)
     {
     /* add directory levels, using training digits for names */
     char fcntStr[64], dirBuf[3];
     int i, iDir;
     safef(fcntStr, sizeof(fcntStr), "%0*d", outDirDepth, fileCount);
     iDir = strlen(fcntStr)-outDirDepth;
     strcpy(dirBuf, "X/");
     for (i = 0; i < outDirDepth; i++, iDir++)
         {
         dirBuf[0] = fcntStr[iDir];
         strcat(outPath, dirBuf);
         makeDir(outPath);
         }
     }
 
 if (digits)
     sprintf(outPath+strlen(outPath), "%s%0*d.fa", fname, digits, fileCount);
 }
 
 void splitByBase(char *inName, int splitCount, char *outRoot, off_t estSize)
 /* Split into a file base by base. */
 {
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 int lineSize;
 char *line;
 char c;
 char dir[PATH_LEN], seqName[128], outFile[128], outPathName[PATH_LEN];
 int digits = digitsBaseTen(splitCount);
 boolean warnedMultipleRecords = FALSE;
 int fileCount = 0;
 off_t nextEnd = 0;
 off_t curPos = 0;
 FILE *f = NULL;
 int linePos = 0;
 int outLineSize = 50;
 
 
 if (!lineFileNext(lf, &line, &lineSize))
     errAbort("%s is empty", inName);
 if (line[0] == '>')
     {
     line = firstWordInLine(line+1);
     if (line == NULL)
         errAbort("Empty initial '>' line in %s", inName);
     strncpy(seqName, line, sizeof(seqName));
     }
 else
     {
     splitPath(inName, dir, seqName, NULL);
     lineFileReuse(lf);
     }
 splitPath(outRoot, NULL, outFile, NULL);
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] == '>')
         {
 	if (!warnedMultipleRecords)
 	    {
 	    warnedMultipleRecords = TRUE;
 	    warn("More than one record in FA file line %d of %s", 
 	    	lf->lineIx, lf->fileName);
 	    continue;
 	    }
 	}
     while ((c = *line++) != 0)
         {
 	if (isdigit(c) || isspace(c))
 	    continue;
 	if (!isalpha(c))
 	    errAbort("Weird %c (0x%x) line %d of %s", c, c, lf->lineIx, lf->fileName);
 	if (++curPos >= nextEnd)
 	    {
 	    if (f != NULL)
 	        {
 		if (linePos != 0)
 		    fputc('\n', f);
 		fclose(f);
 		}
             mkOutPath(outPathName, outRoot, digits, fileCount);
 	    verbose(2, "writing %s\n", outPathName);
 	    f = mustOpen(outPathName, "w");
 	    fprintf(f, ">%s%0*d\n", outFile, digits, fileCount);
 	    ++fileCount;
 	    linePos = 0;
 	    nextEnd = calcNextEnd(fileCount, splitCount, estSize);
 	    }
 	fputc(c, f);
 	if (++linePos >= outLineSize)
 	    {
 	    fputc('\n', f);
 	    linePos = 0;
 	    }
 	}
     }
 if (f != NULL)
     {
     if (linePos != 0)
 	fputc('\n', f);
     fclose(f);
     }
 lineFileClose(&lf);
 }
 
 void splitByRecord(char *inName, int splitCount, char *outRoot, off_t estSize)
 /* Split into a file base by base. */
 {
 struct dnaSeq seq;
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 int digits = digitsBaseTen(splitCount);
 off_t nextEnd = 0;
 off_t curPos = 0;
 int fileCount = 0;
 FILE *f = NULL;
 char outPath[PATH_LEN];
 ZeroVar(&seq);
 
 while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
     {
     curPos += seq.size;
     if (curPos > nextEnd)
         {
 	carefulClose(&f);
         mkOutPath(outPath, outRoot, digits, fileCount++);
 	verbose(2, "writing %s\n", outPath);
 	f = mustOpen(outPath, "w");
 	nextEnd = calcNextEnd(fileCount, splitCount, estSize);
 	}
     faWriteNext(f, seq.name, seq.dna, seq.size);
     }
 carefulClose(&f);
 lineFileClose(&lf);
 }
 
 void splitAbout(char *inName, off_t approxSize, char *outRoot)
 /* Split into chunks of about approxSize.  Don't break up
  * sequence though. */
 {
 struct dnaSeq seq;
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 int digits = 2;
 off_t curPos = approxSize;
 int fileCount = 0;
 FILE *f = NULL;
 char outPath[PATH_LEN];
 ZeroVar(&seq);
 
 while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
     {
     if (curPos >= approxSize)
         {
 	carefulClose(&f);
 	curPos = 0;
         mkOutPath(outPath, outRoot, digits, fileCount++);
 	verbose(2, "writing %s\n", outPath);
 	f = mustOpen(outPath, "w");
 	}
     curPos += seq.size;
     faWriteNext(f, seq.name, seq.dna, seq.size);
     }
 carefulClose(&f);
 lineFileClose(&lf);
 }
 
 void splitByName(char *inName, char *outRoot)
 /* Split into chunks using sequence names.  */
 {
 struct dnaSeq seq;
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 FILE *f = NULL;
 char outDir[256], outFile[128], ext[64], outPath[512];
 ZeroVar(&seq);
 
 splitPath(outRoot, outDir, outFile, ext);
 
 while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
     {
     carefulClose(&f);
     if (outDirDepth > 0)
 	{
 	char *ptr;
 
 	for(ptr=&seq.name[strlen(seq.name) - 1]; isdigit(*ptr); ptr--)
 	    ;
 	if (ptr > &seq.name[strlen(seq.name)])
 	    errAbort("outDirDepth specified but sequence name doesn't have any digits");
 
 	ptr++;
 	mkOutPath(outPath, outRoot, 0, atoi(ptr));
 	safef(outPath+strlen(outPath), sizeof(outPath) - strlen(outPath), "%s.fa", seq.name);
 	}
     else
 	sprintf(outPath, "%s%s.fa", outDir, seq.name);
     verbose(2, "writing %s\n", outPath);
     f = mustOpen(outPath, "w");
     faWriteNext(f, seq.name, seq.dna, seq.size);
     }
 carefulClose(&f);
 lineFileClose(&lf);
 }
 
 void splitByNamePrefix(char *inName, char *outRoot, int preFixCount)
 /* Split into chunks using prefix of sequence names.  */
 {
 struct dnaSeq seq;
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 FILE *f = NULL;
 char outDir[256], outFile[128], ext[64], outPath[512], preFix[512];
 ZeroVar(&seq);
 
 splitPath(outRoot, outDir, outFile, ext);
 assert(preFixCount < sizeof(preFix));
 
 while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
     {
     carefulClose(&f);
     strncpy(preFix, seq.name, preFixCount);
     preFix[preFixCount] = '\0';
     sprintf(outPath, "%s%s.fa", outDir, preFix);
     verbose(2, "writing %s\n", outPath);
     f = mustOpen(outPath, "a");
     faWriteNext(f, seq.name, seq.dna, seq.size);
     }
 carefulClose(&f);
 lineFileClose(&lf);
 }
 int countN(char *s, int size)
 /* Count number of N's from s[0] to s[size-1].
  * Treat any parts past end of string as N's. */
 {
 int goodCount = 0;
 int i;
 char c;
 
 for (i=0; i<size; ++i)
     {
     c = s[i];
     if (c == 0)
         break;
     if (c != 'n')
         ++goodCount;
     }
 return size - goodCount;
 }
 
 void bitsForOut(char *fileName, int seqSize, Bits *bits)
 /* Get bitmap that corresponds to outFile. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line, *words[8];
 int wordCount;
 boolean firstTime = TRUE;
 int start,end;
 
 /* Check and skip over three line header */
 if (!lineFileNext(lf, &line, NULL))
     errAbort("%s is empty", fileName);
 line = skipLeadingSpaces(line);
 if (!startsWith("SW", line))
     errAbort("%s is not a RepeatMasker .out file", fileName);
 lineFileNext(lf, &line, NULL);
 if (!startsWith("score", line))
     errAbort("%s is not a RepeatMasker .out file", fileName);
 lineFileNext(lf, &line, NULL);
 
 for (;;)
     {
     if (!lineFileNext(lf, &line, NULL))
         break;
     wordCount = chopLine(line, words);
     if (wordCount < 8)
 	errAbort("Short line %d of %s\n", lf->lineIx, lf->fileName);
     start = lineFileNeedNum(lf, words, 5) - 1;
     end = lineFileNeedNum(lf, words, 6);
     if (start > end)
         errAbort("Start after end line %d of %s", lf->lineIx, lf->fileName);
     if (firstTime)
         {
 	char *s = words[7];
 	if (s[0] != '(' || !isdigit(s[1]))
 	    errAbort("Expected parenthesized number line %d of %s", lf->lineIx, lf->fileName);
 	if (seqSize != end + atoi(s+1))
 	    errAbort("Size mismatch line %d of %s", lf->lineIx, lf->fileName);
 	firstTime = FALSE;
 	}
     if (end > seqSize)
         errAbort("End past bounds line %d of %s", lf->lineIx, lf->fileName);
     bitSetRange(bits, start, end-start);
     }
 lineFileClose(&lf);
 }
 
 void setBitsN(DNA *dna, int size, Bits *bits)
 /* Set bits in bitmap where there are N's in DNA. */
 {
 int i;
 for (i=0; i<size; ++i)
     {
     if (dna[i] == 'n' || dna[i] == 'N')
 	bitSetOne(bits, i);
     }
 }
 
 void splitByCount(char *inName, int pieceSize, char *outRoot, off_t estSize, int extra)
 /* Split up file into pieces pieceSize long. */
 {
 off_t pieces = (estSize + pieceSize-1)/pieceSize;
 int digits = digitsBaseTen(pieces);
 int maxN = optionInt("maxN", pieceSize-1);
 boolean oneFile = optionExists("oneFile");
 char fileName[PATH_LEN];
 char dirOnly[PATH_LEN], noPath[128];
 int pos, pieceIx = 0, writeCount = 0;
 struct dnaSeq seq;
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 FILE *f = NULL;
 Bits *bits = NULL;
 int seqCount = 0;
 char *outFile = optionVal("out", NULL);
 char *liftFile = optionVal("lift", NULL);
 FILE *lift = NULL;
 ZeroVar(&seq);
 
 splitPath(outRoot, dirOnly, noPath, NULL);
 if (oneFile)
     {
     sprintf(fileName, "%s.fa", outRoot);
     f = mustOpen(fileName, "w");
     }
 if (liftFile)
     lift = mustOpen(liftFile, "w");
 
 
 /* Count number of N's from s[0] to s[size-1].
  * Treat any parts past end of string as N's. */
 while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
     {
     bits = bitAlloc(seq.size);
     setBitsN(seq.dna, seq.size, bits);
     ++seqCount;
     if (outFile != NULL)
         {
 	if (seqCount > 1)
 	    errAbort("Can only handle in files with one sequence using out option");
 	bitsForOut(outFile, seq.size, bits);
 	}
     for (pos = 0; pos < seq.size; pos += pieceSize)
         {
 	char numOut[128];
 	int thisSize = seq.size - pos;
 	if (thisSize > (pieceSize + extra)) 
 	    thisSize = pieceSize + extra;
 	if (bitCountRange(bits, pos, thisSize) <= maxN)
 	    {
 	    if (!oneFile)
 	        {
                 mkOutPath(fileName, outRoot, digits, pieceIx);
 		f = mustOpen(fileName, "w");
 		}
             sprintf(numOut, "%s%0*d", noPath, digits, pieceIx);
 	    faWriteNext(f, numOut, seq.dna + pos, thisSize);
 	    if (lift)
 	        fprintf(lift, "%d\t%s\t%d\t%s\t%d\n",
 		    pos, numOut, thisSize, seq.name, seq.size);
 	    ++writeCount;
 	    if (!oneFile)
 	        carefulClose(&f);
 	    }
         pieceIx++;
 	}
     bitFree(&bits);
     }
 carefulClose(&f);
 carefulClose(&lift);
 lineFileClose(&lf);
 printf("%d pieces of %d written\n", writeCount, pieceIx);
 }
 
 boolean findLastGap(DNA *dna, int stopOffset, int endOffset, int minGapSize,
 		    int *retGapStart, int *retGapSize)
 /* Find the last gap (block of at least minGapSize N's) in dna that starts 
  * before stopOffset.  If we reach stopOffset while in a block of N's, keep 
  * counting N's unless we hit endOffset.  If a gap is found, return true. */
 {
 boolean gotGap = FALSE;
 int gapStart = 0;
 int gapSize = 0;
 int nStart = 0;
 int nSize = 0;
 int i = 0;
 
 for (i=0;  i < stopOffset;  i++)
     {
     if (dna[i] == 'n' || dna[i] == 'N')
 	{
 	if (nSize == 0)
 	    nStart = i;
 	nSize++;
 	}
     else
 	{
 	if (nSize > 0)
 	    {
 	    if (nSize > minGapSize)
 		{
 		gotGap   = TRUE;
 		gapStart = nStart;
 		gapSize  = nSize;
 		}
 	    nSize = 0;
 	    }
 	}
     }
 
 if (nSize > 0)
     {
     while ((dna[i] == 'n' || dna[i] == 'N') &&
 	   i < endOffset)
 	{
 	nSize++;
 	i++;
 	}
     if (nSize > minGapSize)
 	{
 	gotGap   = TRUE;
 	gapStart = nStart;
 	gapSize  = nSize;
 	}
     }
 
 *retGapStart = gapStart;
 *retGapSize  = gapSize;
 return(gotGap);
 }
 
 static void writeOneByGap(boolean oneFile, char *outRoot,
     int digits, int *pieceIx, FILE *f, char noPath[256], int pos, int thisSize,
 	struct dnaSeq *seq, FILE *lift, int *writeCount, char *outPath)
 {
 char numOut[128];
 if (!oneFile)
     {
     char fileName[512];
     mkOutPath(fileName, outRoot, digits, *pieceIx);
     f = mustOpen(fileName, "w");
     verbose(2, "writing %s\n", fileName);
     }
 else
     verbose(2, "writing %s\n", outPath);
 sprintf(numOut, "%s%0*d", noPath, digits, *pieceIx);
 verbose(3,"#\twriting piece %s, at pos %d for size %d\n", numOut,pos,thisSize);
 faWriteNext(f, numOut, seq->dna + pos, thisSize);
 if (lift)
     fprintf(lift, "%d\t%s\t%d\t%s\t%d\n",
 	pos, numOut, thisSize, seq->name, seq->size);
 *writeCount += 1;
 *pieceIx += 1;
 if (!oneFile)
     carefulClose(&f);
 }
 
 void splitByGap(char *inName, int pieceSize, char *outRoot, long long estSize)
 /* Split up file into pieces at most pieceSize bases long, at gap boundaries 
  * if possible. */
 {
 off_t pieces = (estSize + pieceSize-1)/pieceSize;
 int digits = digitsBaseTen(pieces);
 int minGapSize = optionInt("minGapSize", 1000);
 boolean noGapDrops = optionExists("noGapDrops");
 int maxN = optionInt("maxN", pieceSize-1);
 boolean oneFile = optionExists("oneFile");
 char fileName[512];
 char dirOnly[256], noPath[128];
 int pos, pieceIx = 0, writeCount = 0;
 struct dnaSeq seq;
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 FILE *f = NULL;
 Bits *bits = NULL;
 int seqCount = 0;
 char *outFile = optionVal("out", NULL);
 char *liftFile = optionVal("lift", NULL);
 FILE *lift = NULL;
 ZeroVar(&seq);
 
 if (minGapSize < 1)
     errAbort("ERROR: minGapSize must be > 0");
 
 splitPath(outRoot, dirOnly, noPath, NULL);
 if (oneFile)
     {
     sprintf(fileName, "%s.fa", outRoot);
     f = mustOpen(fileName, "w");
     }
 else
     fileName[0] = '\0';
 if (liftFile)
     lift = mustOpen(liftFile, "w");
 
 while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
     {
     bits = bitAlloc(seq.size);
     setBitsN(seq.dna, seq.size, bits);
     ++seqCount;
     if (outFile != NULL)
         {
 	if (seqCount > 1)
 	    errAbort("Can only handle in files with one sequence using out option");
 	bitsForOut(outFile, seq.size, bits);
 	}
     pos = 0;
     while (pos < seq.size)
         {
 	boolean gotGap = FALSE;
 	int gapStart = 0;
 	int gapSize  = 0;
 	int endSize  = seq.size - pos;
 	int thisSize = min(endSize, pieceSize);
 	int startGapLen = 0;
 
 	if (seq.dna[pos] == 'n' || seq.dna[pos] == 'N')
 	    {
 	    startGapLen = bitFindClear(bits, pos, endSize) - pos;
 	    verbose(3,"#\tstarting gap at %d for length: %d\n", pos,
 		startGapLen );
 	    }
 	/*	if a block is all gap for longer than minGapSize, then
  	 *	keep it all together in one large piece
 	 */
 	if (startGapLen > minGapSize)
 	    {
 	    if (noGapDrops)
 		{
 		writeOneByGap(oneFile, outRoot, digits, &pieceIx,
 		    f, noPath, pos, startGapLen, &seq, lift,
 			&writeCount, fileName);
 		}
 	    else
 		verbose(3,"#\tbeginning gap of %d size skipped\n", startGapLen);
 	    thisSize = startGapLen;
 	    }
 	else if (thisSize > 0 && bitCountRange(bits, pos, thisSize) <= maxN)
 	    {
 	    if (endSize>pieceSize) /* otherwise chops tiny piece at very end */
 	      {
 		gotGap = findLastGap(&(seq.dna[pos]), thisSize, endSize,
 				     minGapSize, &gapStart, &gapSize);
 		if (gotGap)
 		  thisSize = gapStart;
 	      }
 	    writeOneByGap(oneFile, outRoot, digits, &pieceIx,
 		f, noPath, pos, thisSize, &seq, lift, &writeCount, fileName);
 	    }
 	pos += thisSize;
 	if (gotGap)
 	    {
 	    /*	last block is all gap, write it all out	*/
 	    /*if ((pos + gapSize) >= seq.size)*/
 	    if (noGapDrops)
 		{
 		writeOneByGap(oneFile, outRoot, digits, &pieceIx,
 		    f, noPath, pos, gapSize, &seq ,lift, &writeCount, fileName);
 		verbose(3,
 		    "#\tadding gapSize %d to pos %d -> %d and writing gap\n",
 			gapSize, pos, pos+gapSize);
 		}
 	    else
 		verbose(3,"#\tadding gapSize %d to pos %d -> %d\n",
 			gapSize, pos, pos+gapSize);
 	    pos += gapSize;
 	    }
 	}
     bitFree(&bits);
     }
 carefulClose(&f);
 carefulClose(&lift);
 lineFileClose(&lf);
 printf("%d pieces of %d written\n", writeCount, pieceIx);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 off_t estSize;
 char *how = NULL;
 char *inName = NULL;
 int count;
 char *outRoot;
 int prefixLength = 0;
 int extra = 0;
 
 optionInit(&argc, argv, optionSpecs);
 how = argv[1];
 inName = argv[2];
 
 if (argc < 4 )
     usage();
 outDirDepth = optionInt("outDirDepth", 0);
 prefixLength = optionInt("prefixLength", prefixLength);
 extra = optionInt("extra", extra);
 
 if (sameWord(how, "byname"))
     {
     if (argc != 4)
         usage();
     dnaUtilOpen();
     outRoot = argv[3];
     if (optionExists("prefixLength"))
         {
         /* no count argument.  Make as many as needed */
         splitByNamePrefix(inName, outRoot, prefixLength);
         }
     else
         {
         /* no count argument.  Make as many as needed */
         splitByName(inName, outRoot);
         }
     }
 else
     {
     if (argc != 5 || !isdigit(argv[3][0]))
 	usage();
 
     dnaUtilOpen();
     count = atoi(argv[3]);
     outRoot=argv[4];
     estSize = estimateFaSize(argv[2]);
     if (sameWord(how, "sequence"))
 	splitByRecord(inName, count, outRoot, estSize);
     else if (sameWord(how, "base"))
 	splitByBase(inName, count, outRoot, estSize);
     else if (sameWord(how, "size"))
 	splitByCount(inName, count, outRoot, estSize, extra);
     else if (sameWord(how, "about"))
 	splitAbout(inName, count, outRoot);
     else if (sameWord(how, "gap"))
 	splitByGap(inName, count, outRoot, estSize);
     else
 	usage();
     }
 return 0;
 }

